‘Bones’ Boss on the Season Finale’s Shocking Return: ‘The Story is Not Fully Told Yet’

Warning! This post contains major, major, major spoilers for the Bones season finale. Do not read ahead unless you’ve watched the hour.

Bones‘ latest serial killer, the Puppeteer, has manipulated Booth (David Boreanaz), Brennan (Emily Deschanel), the FBI and the Jeffersonian at every turn, but the Season 11 finale provided the biggest clue to date about who might be responsible for the deaths.

After Brennan was plagued by nightmares of being terrorized in the lab, the worst happened: she was confronted by an unknown person, and (seemingly) taken. As Booth and the team struggled to figure out who could have been haunting Brennan’s dreams—and who could be the killer based on their current evidence—they came to a horrifying conclusion: the signs pointed to it being Zack Addy (Eric Millegan), who worked at the Jeffersonian until it was revealed he worked with another serial killer, Gormogon. (Only the deceased Sweets (John Francis Daley) knew the truth: Zack never actually killed anyone, but he allowed himself to be locked up anyway due to his guilt over his association.)

Indeed by the end of the hour, Zack was with Brennan, and he told her they needed to talk. But is he actually a serial killer now? “He’s a manipulative bastard,” Bones executive producer Michael Peterson warned before the hour of the Puppeteer. “He is in control the entire time. He wants you to assume things that might not be true.”

Peterson dished on the decision to bring Zack back for the first time since 2010 (Millegan was a series regular from 2005-2008), what this will mean for the team, and what’s in store for the 12th and final season. (And read what Millegan had to say about his return here.)

At what point did the discussion start to have Zack return to the show tied to this new serial killer?
Michael Peterson: Probably about mid-year, as we started to look at the arc for this killer. There was a phone call made to [creator] Hart [Hanson]. Not to give too much away, but I think the key was not so much of making Zack the killer, as bringing Zack back. The story for this killer and for Zack is not done yet. Again, the killer is manipulative. He wants you to think one thing, be careful of assumptions.

Just to clarify, can you confirm whether Zack is the killer or this is another manipulation?
Peterson: Before [fans get upset], “You brought him back in this manner?!” I would say, certainly at the end, that’s all appearances [indicate he’s gone dark], and that’s what it should appear to be [in this episode]. But the story is not fully told yet.

I think that should be the question. Is he really? We’re going to have to wait for [Season 12]. There are hints; the astute viewer will pick up clues in both directions, if he did or he didn’t.

What was the cast’s reaction when they heard about the twist?
Peterson: I called up David and Emily ahead of time to tell them what we were planning. Season 12 is really about wrapping up these storylines that really needed to be resolved. There’s some stuff with Booth and Brennan, some stuff that was started back in Season 1. One of the ones that always felt like we needed to tie up very nicely was the Zack storyline. We hadn’t seen him in a while, he’s a fan-favorite, he’s a favorite of mine. I was a fan of the show before I was a writer of the show. I want to resolve Zack in the correct way. That was a goal, that was something David and Emily understood fully; they’re behind it 100 percent. But they knew way ahead of time about the twist coming at the end. Everybody had fun with it! It’s nice to surprise the cast and crew even in Season 11.

How much will Sweets being the sole person to know the truth about Zack not killing anyone play into this arc?
Peterson: That will be a huge part of it. The only person who knew the truth behind Zack’s [relationship with Gormogon] was Sweets; Sweets is dead. And so, that’s something we want to resolve in this final season: let the truth be known and see what happens as a result of it. Absolutely. It will come out: everything that happened that was only revealed to Sweets. The journey of Booth and Brennan hearing the “truth”—but will they believe it?

Related: How Bones’ newest serial killer was inspired by an iconic episode of The X-Files

Zack’s spent a lot of time in a facility he probably shouldn’t have been in. Even without killing anyone, arguably, that could do a huge amount of damage to someone. What can you say about the Zack we’ll see in Season 12?
Peterson: I think that’s the big question: everyone is looking at him, when we come back next season–what has happened? If you look at the very end [of the finale], he has a very large scar across his forehead: what’s the story behind that? He’s been gone for a long, long time. As you very astutely said, being in a place where you’re considered sick will have an impact on him. Who has he been hanging out with, what have their influences been? All of those things will need to be resolved.

The team has had so many threats over the show’s run, but when they’re going after someone who was one of their own, what can you say about their mindset as they’re trying to save Brennan from Zack? Especially someone like Hodgins (TJ Thyne), who was his best friend?
Peterson: Hodgins, as I’m writing the opener, because of his closeness to Zack, he’s handling this in a different way than anyone else. I think we’re seeing a little more of that angry Hodgins coming back. There’s a rage to him, where it’s like the “fool me once” kind of thing; he’s already been through this. He’s been with this with Zack the first time in his mind. Now it seems to be happening again. There is a true anger. At the end of the season, he’s feeling pain in his legs as the nerves are coming back.  But the pain and the anguish with Zack is a thousand times worse than anything physical going on. In a way, it puts things into an odd kind of perspective. This was his best friend, and I don’t think he’s really recovered from the betrayal the first time around. And now as it’s coming back, this is as challenging as anything can be for Hodgins.

Related: Bones boss on Hodgins’ health twist

Hodgins second-guessed the evidence in the finale. Is anyone second-guessing this could be Zack when the show returns? Or because it appears Brennan is in danger, is there no room for that?
Peterson: The first thing is can we get to Brennan in time? That’s the first concern. Once that has been achieved, all the evidence points to him. But again, we’re dealing with a manipulative killer; are we being misled? There are some questions, but most everyone thinks this is Zack 2.0. This is even a worse manifestation of what they had to deal with the first time around. That’s their perspective. But of course, they didn’t know what Sweets knows.

Though Zack has been gone for years, the show did bring him up during the recent documentary episode. How much of that was done to subconsciously remind people of this character who had been MIA for six years, but was about to become a very big factor?
Peterson: That was a very purposeful plant. That was one of those things where we knew it was going to come up in the finale. Zack wasn’t in the first draft of the script, but I went to the writer, Keith [Foglesong], and said, “Hey, let’s make sure to do a mention, and get some still photos we can put up. Not just mention him, but show his face and give that reminder to everybody.” That seemed to work. On Twitter, everyone was so glad for the mention of Zack; I don’t think they quite realized what was coming up.

Looking ahead to 12, Cam (Tamara Taylor) and Arastoo (Pej Vahdat) are getting married. Do you anticipate that happening before the series finale?
Peterson: The way we’re eying it right now is it probably won’t be the series finale. We’ll have so many storylines we’ll have to deal with during the course of 12 episodes. I think we’re going to try and get it somewhere in the midseason. But that could change.

Will there still be episodic cases to solve every episode?
Peterson: I think we’ll always have our crime of the week, even if it’s smaller. I think a perfect example of that was the [Booth and Brennan] wedding episode. It was a relatively small case, but it was mostly character stuff.

Related: Hart Hanson on returning to write the Bones finale

What else do you have planned about Season 12 at this point?
Peterson: When we went in originally to Fox to pitch what we wanted to do, there’s a new threat to Booth and Brennan, it’s something that’s actually borne out of Season 1. A lot of it has to do with the ghosts of the past, if you will. Booth’s arc is really about him seeking forgiveness, in a way, of the sins of the past; the kills he did back when he was a sniper. We’re going to have someone from Booth’s past pay him a visit and haunt him in an interesting way. We really are looking to resolve that. For Brennan, when we first meet her back in Season 1, it was all about finding her family. There are going to be some new twists and turns for Brennan as far as her search for family. We’re looking to resolve Booth dealing with his past sins, if you will, and Brennan’s quest to feel complete with her family. Those will be the big challenges in Season 12.

Brennan’s brother, Russ (Loren Dean), has been away for a bit, since his portrayer no longer acts. Is there a chance he might pop up next season?
Peterson: I don’t know. My ideal situation—and a lot of this is cast-contingent—our goal for Season 12 is for every episode to bring back somebody we haven’t seen in a while. And just really give the proper salute to the fans who have been there since the beginning. We’ll bring back some unexpected faces.

Could that include Season 1’s Goodman (Jonathan Adams)?
Peterson: Everybody’s a possibility. There are dream lists; I’d love that Stephen Fry back. It’s all dependent on who is working on what show. We try to be flexible, but we have our dream lists.

Anything else you can say about the final season?
Peterson: It really is about the fans. We know we’re taking them on a roller coaster ride for the finale, and they have to wait a long time for resolution for it. But trust us. It’s a wild ride, but you’re going to like where it ends up.

Bones returns in 2017.